15:56:42 <RRSAgent> RRSAgent has joined #hcls
15:56:42 <RRSAgent> logging to http://www.w3.org/2010/03/08-hcls-irc
15:56:50 <kei> Zakim, this will be BioRDF
15:56:50 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 4 minutes
15:57:09 <kei> agenda+ introduction [Kei]
15:57:25 <kei> agenda+ iphone app [Don]
15:57:35 <kei> agenda+ microarray use case [All]
15:57:50 <kei> agenda+ cross-task/cross-community activities [All]
15:57:59 <kei> Zakim, take up next agendum
15:57:59 <Zakim> agendum 2. "C-SHALS" taken up [from ericP]
16:00:10 <michael> michael has joined #hcls
16:00:33 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
16:00:40 <Zakim> +mscottm
16:01:12 <Zakim> +Kei_Cheung
16:01:54 <Zakim> +??P17
16:01:59 <Donald_Doherty> Donald_Doherty has joined #HCLS
16:02:25 <Zakim> +[IPcaller]
16:02:34 <Zakim> +michael
16:02:50 <Zakim> +jun
16:02:59 <mscottm> Zakim, +??P17 is matthias
16:02:59 <Zakim> sorry, mscottm, I do not recognize a party named '+??P17'
16:03:00 <jun> jun has joined #hcls
16:03:03 <mscottm> Zakim, ??P17 is matthias
16:03:03 <Zakim> +matthias; got it
16:03:07 <Zakim> +michael.a
16:03:41 <matthias_samwald> matthias_samwald has joined #hcls
16:03:42 <kei> scribenick Matthias
16:03:54 <Zakim> +Don_Doherty
16:04:00 <mscottm> Zakim, who is here?
16:04:00 <Zakim> On the phone I see mscottm, Kei_Cheung, matthias, [IPcaller], michael, jun, michael.a, Don_Doherty
16:04:02 <Zakim> On IRC I see matthias_samwald, jun, Donald_Doherty, michael, RRSAgent, kei, mscottm, Zakim, ericP
16:04:37 <rfrost> rfrost has joined #HCLS
16:05:06 <matthias_samwald> kei: agenda will start with don's demo of his iPhone app
16:05:24 <Donald_Doherty> Download slides from:
16:05:26 <Donald_Doherty> http://www.actionpotential.com/SemanticWb_beta2_1.pdf
16:05:31 <matthias_samwald> ... then we will go on to the microarray use-case and discussion of cross-task activities
16:06:00 <kei> http://www.actionpotential.com/SemanticWb_beta2_1.pdf 
16:06:38 <mscottm> Zakim, take up next agendum
16:06:38 <Zakim> agendum 4. "introduction" taken up [from Kei]
16:07:29 <matthias_samwald> TOPIC -- Don's iPhone Application
16:07:56 <matthias_samwald> don: slides are at http://www.actionpotential.com/SemanticWb_beta2_1.pdf 
16:08:36 <matthias_samwald> ... if you go to iTunes and donwload the "SemanticWb" application, you can choose between SPARQL endpoints
16:08:47 <matthias_samwald> ... i will be using the Neurocommons endpoint
16:09:02 <matthias_samwald> ... i will show version 2.1, which will soon be available
16:09:45 <matthias_samwald> ... you have to run the application on the iPhone / iPod Touch / iPad, you cannot run it through iTunes directly
16:10:21 <Bin> Bin has joined #hcls
16:10:31 <jun> zakim,mute me
16:10:31 <Zakim> jun should now be muted
16:11:18 <Zakim> + +1.617.768.aaaa
16:11:19 <matthias_samwald> don: you can do a lot with a central server where you aggregate everything, but what could i do with accessing SPARQL endpoints? 
16:11:34 <matthias_samwald> ... you cannot do complex calculations or reasoning on an iPhone
16:11:50 <matthias_samwald> ... to start, you type in something interesting.
16:11:58 <matthias_samwald> ... autocomplete turned out to be too slow
16:12:05 <Bin> Bin has joined #hcls
16:12:12 <matthias_samwald> ... MeSH terminology is integrated into the system
16:12:29 <sudeshna> sudeshna has joined #hcls
16:12:54 <matthias_samwald> ... search gives you MeSH results
16:14:30 <matthias_samwald> ... you can navigate to proteins (e.g., amyloid beta)
16:14:35 <matthias_samwald> ... from there to articles
16:15:34 <sudeshna> Hi! Ti asked me to join the call - can you please send a pointer to the presenatation?
16:15:41 <matthias_samwald> ... associated genes [slide 10]
16:15:46 <matthias_samwald> http://www.actionpotential.com/SemanticWb_beta2_1.pdf 
16:15:55 <matthias_samwald> that is the link, sudeshna
16:16:10 <sudeshna> Thanks!
16:16:34 <Zakim> + +1.937.775.aabb
16:16:47 <matthias_samwald> ... association of genes, gene products...
16:17:06 <ssahoo2> ssahoo2 has joined #HCLS
16:18:17 <matthias_samwald> don: ... summary of information about a protein, acess to UniProt website, structure data
16:20:37 <matthias_samwald> ... structure data and images can be browsed
16:21:33 <matthias_samwald> ... including 3d views
16:21:49 <mscottm> <applause>
16:21:52 <matthias_samwald> don: the newest version will be available on iTunes in 1-2 weeks
16:22:20 <matthias_samwald> kei: this is interesting and impressive, gives people  a feel of what can be done on an iPhone.
16:25:15 <matthias_samwald> kei: have you thought about adding links to podcasts etc.?
16:25:50 <matthias_samwald> don: not yet, but great idea
16:27:00 <matthias_samwald> kei: other ideas: scientific newsfeeds? using the iPhone during meetings and conferences?
16:28:35 <matthias_samwald> don: yes, quickly looking up something during meetings is important
16:30:14 <Zakim> -matthias
16:30:47 <Zakim> +??P17
16:31:13 <Zakim> -??P17
16:31:38 <mscottm> scott: It would be nice to add a tab that integrates the BioRDF microarray use case in a generic way.
16:31:57 <matthias_samwald> matthias_samwald has joined #hcls
16:32:12 <Zakim> +??P17
16:32:42 <matthias_samwald> but i'm back.
16:32:50 <matthias_samwald> zakim, ??P17 is matthias_samwald
16:32:50 <Zakim> +matthias_samwald; got it
16:32:51 <mscottm> thanks for coming back :)
16:33:28 <mscottm> ..Specific idea (if possible?): add a 'data tab' next to the existing tabs that allows you see gene lists from specific microarray data sets within the context of Alzheimer's Disease.
16:34:05 <matthias_samwald> who is talking? i can take over scribing again.
16:34:32 <mscottm> Michael Miller
16:35:19 <matthias_samwald> michael: bioconductor could be useful in this context
16:35:45 <mscottm> Michael: mentioned that Misha Kapushesky demo'd a cloud application of BioConductor at an MGED meeting
16:36:30 <matthias_samwald> kei: don, can you create a wiki page for the iPhone app?
16:36:58 <matthias_samwald> don: yes, i will do that.
16:37:41 <Zakim> +??P1
16:38:33 <matthias_samwald> scott: if you could annotate / aTag you own relation and add it to the HCLS or Concept Web Alliance knowledge base (protein a has something to do with protein b etc.), this could be valuable
16:39:57 <matthias_samwald> scott: the idea behind the Concept Wiki, for example, is to find people that have made similar research statements like you 
16:40:40 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext
16:40:53 <matthias_samwald> TOPIC -- Microarray use-case
16:41:56 <matthias_samwald> kei: if you scroll down on http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext you find a long list of provenance terms
16:42:30 <matthias_samwald> ... i used the NCBO Biomedical Annotator on Pubmed abstracts and experiment texts to identify terms
16:43:32 <matthias_samwald> ... we also identify some provenance ontologies -- Provenir, MGED, NIF etc.
16:45:13 <matthias_samwald> ... gene lists represent a nice use-case for provenance information
16:45:58 <matthias_samwald> ... gene lists are not treated as a standard submission for microarray databases, we could work with MGED to make this part of the standard submission process (in addition to raw data)
16:48:01 <matthias_samwald> scott: people know that there is a need for disclosing gene lists, this would be a good extension for MAGE-TAB, but there is also a policy decision if MGED requires the disposition of this data
16:48:35 <matthias_samwald> ... decisions on this might be made during the next MGED meeting.
16:49:35 <matthias_samwald> michael: one of the things about MGED, which started out as a grass-roots organization: people are enthusiastic, but realization can be tricky.
16:49:59 <matthias_samwald> michael: gene lists are disclosed, but mostly as supplemental data in a non-machine-readable way.
16:50:17 <matthias_samwald> michael: not everything in the paper is useful, even though authors might claim so.
16:52:19 <matthias_samwald> kei: if MGED or MIAME could define a very simple standard/spreadsheet/template, this would already be a small step forward.
16:52:32 <matthias_samwald> michael: it is not a MIAME issue, MIAME does not state a format
16:54:28 <matthias_samwald> sudeshna: MIAME gives you the essential elements, but not more
16:54:57 <matthias_samwald> ... having an entry mask where people enter text and generate RDF this way, this could be useful
16:55:56 <matthias_samwald> ... tim clark was talking to carole goble, linking SWAN to MyExperiment ontology, linking to SWAN claims
16:56:43 <matthias_samwald> kei: with named graphs you could capture some of the provenance information
16:57:04 <matthias_samwald> ... based on your experience, maybe we could come up with a way to represent provenance
16:57:15 <mscottm> Scott: Chris Stoeckert (current MGED board president) suggested the basic requirements for gene list disclosure to be: probe ID (could be a list as multiple probes are often combined and averaged), Gene symbol (could be optional), plus the protocol and parameters used for generating the gene list.
16:57:19 <matthias_samwald> ... to have something concrete to suggest to MGED
16:57:44 <matthias_samwald> ... maybe even a standard Excel format for entry
16:58:13 <matthias_samwald> michael: kei, that is exactly what i was thinking
16:59:11 <matthias_samwald> kei: this would facilitate the cross-task work between BioRDF and Scientific Discourse
17:00:04 <mscottm> Her name is Aedin.
17:01:04 <ssahoo2> I have been contact with Tim Clark regarding a provenance use case from scientific discouse community - I will get back in touch with him
17:02:04 <jun> zakim, unmute me
17:02:04 <Zakim> jun should no longer be muted
17:02:59 <matthias_samwald> scott: last week in boston, kei, tim, I and some other people noted that provenance work was done is several task forces. 
17:03:16 <ericP> jun, i believe you can type "ack me" to be immediately unmuted -- less typing
17:03:35 <jun> great tip, thanks
17:04:03 <matthias_samwald> kei: to make this synergistic, it would be crucial to move this project forward and to make a real impact on the  communities
17:04:24 <matthias_samwald> ... i just came back from an NSF workshop (about visualisation)
17:05:07 <matthias_samwald> ... the Concept Web Alliance and the VIVO community could also be potentially synergistic
17:05:39 <jun> zakim, mute me
17:05:39 <Zakim> jun should now be muted
17:05:49 <matthias_samwald> ... some people at this workshop were aware of our work
17:06:48 <matthias_samwald> ... people confuse BioRDF and Bio2RDF. want to know about overlap etc.
17:07:20 <matthias_samwald> ... I chatted with Michel, we should try to clarify
17:09:02 <matthias_samwald> rob: there is another group that is comparable to VIVO called eagle-i, less focusing on people, but on research resources, consortium made up of 9 institutions, headed by harvard.
17:09:28 <jun> http://esw.w3.org/topic/HCLS/WWW2010/Workshop
17:09:58 <rfrost> currently collaborating with VIVO, NIF, OBI and BRO groups on ontology dev 
17:10:14 <jun> ack me
17:10:21 <Zakim> - +1.937.775.aabb
17:10:21 <matthias_samwald> kei: we will meet again in two weeks
17:10:22 <Zakim> -Don_Doherty
17:10:22 <Zakim> - +1.617.768.aaaa
17:10:25 <Zakim> -jun
17:10:27 <Zakim> -Kei_Cheung
17:10:27 <matthias_samwald> Zakim, draft notes
17:10:27 <Zakim> I don't understand 'draft notes', matthias_samwald
17:10:30 <Zakim> -michael.a
17:10:34 <mscottm>   RRSAgent, please draft minutes
17:10:34 <RRSAgent> I have made the request to generate http://www.w3.org/2010/03/08-hcls-minutes.html mscottm
17:10:37 <Zakim> -michael
17:10:41 <mscottm>   RRSAgent, please make log world-visible
17:10:42 <Zakim> -[IPcaller]
17:10:44 <Zakim> -??P1
17:10:55 <matthias_samwald> haven't scribed in a while :) thanks, scott.
17:11:04 <Zakim> -matthias_samwald
17:11:35 <mscottm> Zakim, who is here?
17:11:35 <Zakim> On the phone I see mscottm
17:11:37 <Zakim> On IRC I see matthias_samwald, sudeshna, RRSAgent, kei, mscottm, Zakim, ericP
17:11:39 <Zakim> -mscottm
17:11:40 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:11:42 <Zakim> Attendees were mscottm, Kei_Cheung, [IPcaller], michael, jun, matthias, Don_Doherty, +1.617.768.aaaa, +1.937.775.aabb, matthias_samwald
17:13:28 <sudeshna> +1.617.768.aaaa sudeshna
20:03:29 <RRSAgent> RRSAgent has joined #hcls
20:03:29 <RRSAgent> logging to http://www.w3.org/2010/03/08-hcls-irc
20:03:34 <mscottm> try it now
20:03:36 <Zakim> Team_(hcls)20:03Z has now started
20:03:43 <Zakim> +??P5
20:03:44 <Susie> zakim, space for 6?
20:03:44 <Zakim> Susie, an adhoc conference was scheduled here less than 2 minutes ago
20:03:44 <jun> it works now!
20:04:13 <Zakim> + +1.215.628.aaaa
20:04:21 <Zakim> +mscottm
20:04:56 <ericP> zakim, please dial ericP-mobile
20:04:56 <Zakim> ok, ericP; the call is being made
20:04:57 <Zakim> +EricP
20:05:04 <Zakim> +Kei_Cheung
20:05:33 <mscottm> Zakim, disconnect EricP
20:05:33 <Zakim> EricP is being disconnected
20:05:35 <Zakim> -EricP
20:06:00 <mscottm> zakim, please dial ericP-mobile
20:06:00 <Zakim> ok, mscottm; the call is being made
20:06:01 <Zakim> +EricP
20:06:33 <mscottm> Zakim, disconnect EricP
20:06:33 <Zakim> EricP is being disconnected
20:06:35 <Zakim> -EricP
20:12:35 <mscottm> lost audio..
20:12:58 <ericP> network around almaden is hosed
20:13:07 <ericP> can send gprs so i'll type
20:13:19 <mscottm> got audio back
20:24:29 <Zakim> + +1.408.927.aabb
20:53:14 <Zakim> - +1.408.927.aabb
21:08:03 <mscottm> Hilary
21:08:03 <mscottm> Spencer
21:08:18 <mscottm> Hilary Spencer
21:11:03 <Zakim> - +1.215.628.aaaa
21:11:06 <Zakim> -Kei_Cheung
21:11:07 <Zakim> -mscottm
21:11:14 <Zakim> -??P5
21:11:16 <Zakim> Team_(hcls)20:03Z has ended
21:11:17 <Zakim> Attendees were +1.215.628.aaaa, mscottm, EricP, Kei_Cheung, +1.408.927.aabb
23:14:51 <mscottm> mscottm has joined #hcls